My DS2 has had two lots of grommets and adenoids removed. The GP has given you a prescription as a precaution as from what you describe is classic ear infection symptons. Thrashing about and sometimes they will try and hit their head trying to fix it themselves.
As the GP couldn't see the ear drum for the wax, he has left it up to your judgement as to fill the script or not by the sounds of it. As for removal of wax, again a GP usually will not do it on a little one as they don't like to syringe in case it worsens the possible infection.
When I demanded a referral to see an ENT with my DS2, the ENT had a special little hook that just went in and out came ALL the wax, it was amazing. He explained the syringing can sometimes cause an infection if one is not their already. He then saw glue ear and we had our first lot of grommets. It's also quite common for boys in particular as they tend to have short drainage tubes that don't let the wax out.
If you are confident, you could try Hopi Ear Candling if you can get your DS2 stay still long enough, obviously under close monitoring. Another GP did say to try and put drops of olive oil in to see if the wax moves itself. It's worth a try as you sound like you are quite rural.
If you think he is feeling better in himself, then I agree on not giving the antibiotics for just in case. It's a tough one, hope he is feeling better your poor little man